Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra

Abstract

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

Reductive Transformation of 3-Nitro-1,2,4-triazol-5-one (NTO) by Leonardite Humic Acid and Anthraquinone-2,6-disulfonate (AQDS)

“…When NTO is added to a solution containing LHA Red , it would first oxidize hydroquinones having the lowest reduction potentials and move onto hydroquinones of increasing potentials (and decreasing rate constants) as the reaction proceeds, resulting in deviations from the first-order behavior. (2) Physically, humic acid is a structurally dynamic, three-dimensional entity that undergoes constant conformational changes, such as aggregation, dissociation, and folding–unfolding, processes that are influenced by solution conditions such as pH, temperature, and ionic strength. − As a result, only a portion of the total electrons stored in LHA Red would be exposed and accessible to solutes, such as NTO, at any given time. Additional reactive sites (i.e., hydroquinones) would become accessible over time through structural rearrangements of LHA and/or diffusion of NTO into the LHA interior.…”

Relationships between the Physicochemical Properties of Dissolved Organic Matter and Its Reaction with Sodium Borohydride

“…Furthermore, a recent study utilizing molecular dynamics simulations concluded that DOM chromophores, including π−π stacked charge-transfer complexes, are generally solvent-accessible (<10% solvent-inaccessible). 29 Additional support for this idea comes from the study of Ferreira et al, which examined line broadening of hydrophobic stearic acid labeled with a nitroxide free radical (5-SASL). 30 In pH 3 humic substance solution (3 g/L), the electron spin resonance line width of 5-SASL became broader over the course of days, indicating partitioning of this probe into a more viscous, hydrophobic environment.…”

“…For example, a study by Tinnancher and Honeyman utilizing tritiated borohydride to label SRFA reported that tritium was evenly distributed throughout different size fractions of SRFA (as measured by SEC), suggesting that borohydride was able to access and react with all DOM size fractions equally. Furthermore, a recent study utilizing molecular dynamics simulations concluded that DOM chromophores, including π–π stacked charge-transfer complexes, are generally solvent-accessible (<10% solvent-inaccessible) . Additional support for this idea comes from the study of Ferreira et al , which examined line broadening of hydrophobic stearic acid labeled with a nitroxide free radical (5-SASL) .…”

Molecular dynamics simulation of organic contaminant adsorption on organic‐coated smectite clay

“…A potentially promising avenue for future research may be to examine the coating of clay mineral nanoparticles by the more complex SOM proxies recently proposed by Devarajan et al (2020) or Escalona et al (2021). However, we note that for such complex organic mixtures, the short timescale of typical MD simulations may be insufficient to obtain well equilibrated organic coatings, in which case the use of enhanced sampling techniques, such as replica-exchange MD simulations (Atmani et al, 2020;Vialykh et al, 2020), may be required.…”

“…(2021). However, we note that for such complex organic mixtures, the short time‐scale of typical MD simulations may be insufficient to obtain well equilibrated organic coatings, in which case the use of enhanced sampling techniques, such as replica‐exchange MD simulations (Atmani et al., 2020; Vialykh et al., 2020), may be required.…”